rs2333895

Variant names:

• chr4-60277367-A-G
• rs2333895

Your query was ambiguous. Multiple possible variants found:

• chr4-60277367-A-G
• chr4-60277367-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.697 in 151,814 control chromosomes in the GnomAD database, including 38,934 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (38934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105775 AN: 151696 Hom.: 38937 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.724

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.697 AC: 105790 AN: 151814 Hom.: 38934 Cov.: 32 AF XY: 0.693 AC XY: 51430 AN XY: 74194

African (AFR) AF: 0.459 AC: 18982 AN: 41392

American (AMR) AF: 0.767 AC: 11675 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2739 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2564 AN: 5144

South Asian (SAS) AF: 0.600 AC: 2890 AN: 4814

European-Finnish (FIN) AF: 0.795 AC: 8366 AN: 10526

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56099 AN: 67926

Other (OTH) AF: 0.716 AC: 1510 AN: 2108

Alfa AF: 0.779 Hom.: 118000

Bravo AF: 0.688

Asia WGS AF: 0.508 AC: 1764 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.74
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2333895; hg19: chr4-61143085;